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Kanai Y, Harada A, Shibata T, Nishimura R, Namiki K, Watanabe M, Nakamura S, Yumoto F, Senda T, Suzuki A, Neya S, Yamamoto Y. Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor. Biochemistry 2017; 56:4500-4508. [DOI: 10.1021/acs.biochem.7b00457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuki Kanai
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ayaka Harada
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Tomokazu Shibata
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Kosuke Namiki
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Miho Watanabe
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shunpei Nakamura
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Fumiaki Yumoto
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Toshiya Senda
- Structural
Biology Research Center, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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Shibata T, Kanai Y, Nishimura R, Xu L, Moritaka Y, Suzuki A, Neya S, Nakamura M, Yamamoto Y. Characterization of Ground State Electron Configurations of High-Spin Quintet Ferrous Heme Iron in Deoxy Myoglobin Reconstituted with Trifluoromethyl Group-Substituted Heme Cofactors. Inorg Chem 2016; 55:12128-12136. [DOI: 10.1021/acs.inorgchem.6b01360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuki Kanai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Liyang Xu
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuki Moritaka
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of
Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Mikio Nakamura
- Department
of Chemistry, Faculty of Science, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
- Life Science
Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba 305-8577, Japan
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Nishimura R, Shibata T, Tai H, Ishigami I, Yanagisawa S, Ogura T, Neya S, Suzuki A, Yamamoto Y. Effect of the Electron Density of the Heme Fe Atom on the Fe–Histidine Coordination Bond in Deoxy Myoglobin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20130331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - Hulin Tai
- Department of Chemistry, University of Tsukuba
| | - Izumi Ishigami
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Sachiko Yanagisawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University
| | - Akihiro Suzuki
- Department of Materials Engineering, Nagaoka National College of Technology
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Nishimura R, Shibata T, Tai H, Ishigami I, Ogura T, Nagao S, Matsuo T, Hirota S, Imai K, Neya S, Suzuki A, Yamamoto Y. Relationship between the Electron Density of the Heme Fe Atom and the Vibrational Frequencies of the Fe-Bound Carbon Monoxide in Myoglobin. Inorg Chem 2013; 52:3349-55. [DOI: 10.1021/ic3028447] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryu Nishimura
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hulin Tai
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Izumi Ishigami
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School
of Life Science, University of Hyogo, Kamigori-cho,
Ako-gun, Hyogo 678-1297, Japan
| | - Satoshi Nagao
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takashi Matsuo
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Shun Hirota
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kiyohiro Imai
- Department of Frontier Bioscience,
Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo 184-8584, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical
Sciences, Chiba University, Chuoh-Inohana,
Chiba 260-8675, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, Nagaoka National College of Technology, Nagaoka 940-8532, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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Shibata T, Matsumoto D, Nishimura R, Tai H, Matsuoka A, Nagao S, Matsuo T, Hirota S, Imai K, Neya S, Suzuki A, Yamamoto Y. Relationship between oxygen affinity and autoxidation of myoglobin. Inorg Chem 2012; 51:11955-60. [PMID: 23082875 DOI: 10.1021/ic301848t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies using myoglobins reconstituted with a variety of chemically modified heme cofactors revealed that the oxygen affinity and autoxidation reaction rate of the proteins are highly correlated to each other, both decreasing with decreasing the electron density of the heme iron atom. An Fe(3+)-O(2)(-)-like species has been expected for the Fe(2+)-O(2) bond in the protein, and the electron density of the heme iron atom influences the resonance process between the two forms. A shift of the resonance toward the Fe(2+)-O(2) form results in lowering of the O(2) affinity due to an increase in the O(2) dissociation rate. On the other hand, a shift of the resonance toward the Fe(3+)-O(2)(-)-like species results in acceleration of the autoxidation through increasing H(+) affinity of the bound ligand.
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Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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Field-dependent 19F NMR study of sperm whale myoglobin reconstituted with a ring-fluorinated heme. Polym J 2012. [DOI: 10.1038/pj.2012.60] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fluorinated porphyrinoids and their biomedical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2011. [DOI: 10.1016/j.jphotochemrev.2011.09.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Shibata T, Nagao S, Fukaya M, Tai H, Nagatomo S, Morihashi K, Matsuo T, Hirota S, Suzuki A, Imai K, Yamamoto Y. Effect of heme modification on oxygen affinity of myoglobin and equilibrium of the acid-alkaline transition in metmyoglobin. J Am Chem Soc 2010; 132:6091-8. [PMID: 20392104 DOI: 10.1021/ja909891q] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functional regulation of myoglobin (Mb) is thought to be achieved through the heme environment furnished by nearby amino acid residues, and subtle tuning of the intrinsic heme Fe reactivity. We have performed substitution of strongly electron-withdrawing perfluoromethyl (CF(3)) group(s) as heme side chain(s) of Mb to obtain large alterations of the heme electronic structure in order to elucidate the relationship between the O(2) affinity of Mb and the electronic properties of heme peripheral side chains. We have utilized the equilibrium constant (pK(a)) of the "acid-alkaline transition" in metmyoglobin in order to quantitatively assess the effects of the CF(3) substitutions for the electron density of heme Fe atom (rho(Fe)) of the protein. The pK(a) value of the protein was found to decrease by approximately 1 pH unit upon the introduction of one CF(3) group, and the decrease in the pK(a) value with decreasing the rho(Fe) value was confirmed by density functional theory calculations on some model compounds. The O(2) affinity of Mb was found to correlate well with the pK(a) value in such a manner that the P(50) value, which is the partial pressure of O(2) required to achieve 50% oxygenation, increases by a factor of 2.7 with a decrease of 1 pK(a) unit. Kinetic studies on the proteins revealed that the decrease in O(2) affinity upon the introduction of an electron-withdrawing CF(3) group is due to an increase in the O(2) dissociation rate. Since the introduction of a CF(3) group substitution is thought to prevent further Fe(2+)-O(2) bond polarization and hence formation of a putative Fe(3+)-O(2)(-)-like species of the oxy form of the protein [Maxwell, J. C.; Volpe, J. A.; Barlow, C. H.; Caughey, W. S. Biochem. Biophys. Res. Commun. 1974, 58, 166-171], the O(2) dissociation is expected to be enhanced by the substitution of electron-withdrawing groups as heme side chains. We also found that, in sharp contrast to the case of the O(2) binding to the protein, the CO association and dissociation rates are essentially independent of the rho(Fe) value. As a result, the introduction of electron-withdrawing group(s) enhances the preferential binding of CO to the protein over that of O(2). These findings not only resolve the long-standing issue of the mechanism underlying the subtle tuning of the intrinsic heme Fe reactivity, but also provide new insights into the structure-function relationship of the protein.
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Affiliation(s)
- Tomokazu Shibata
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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Shibata T, Nagao S, Tai H, Nagatomo S, Hamada H, Yoshikawa H, Suzuki A, Yamamoto Y. Characterization of the acid–alkaline transition in the individual subunits of human adult and foetal methaemoglobins. J Biochem 2010; 148:217-29. [DOI: 10.1093/jb/mvq055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Affiliation(s)
- Jacques Leroy
- Ecole Normale Supérieure, Département de Chimie, UMR CNRS 8640, 24 rue Lhomond, 75231 Paris Cedex 05, France, Fax: +33‐1‐44322402
| | - Arnaud Bondon
- RMN‐ILP, UMR CNRS 6026, IFR 140, PRISM, Campus de Villejean, CS 34317, Université de Rennes 1, 35043 Rennes Cedex, France
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Nagao S, Hirai Y, Kawano S, Imai K, Suzuki A, Yamamoto Y. Heme orientational disorder in human adult hemoglobin reconstituted with a ring fluorinated heme and its functional consequences. Biochem Biophys Res Commun 2007; 354:681-5. [PMID: 17258177 DOI: 10.1016/j.bbrc.2007.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2006] [Accepted: 01/04/2007] [Indexed: 11/22/2022]
Abstract
A ring fluorinated heme, 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2-fluoro-7,12,18-trimethyl-porphyrinatoiron(III), has been incorporated into human adult hemoglobin (Hb A). The heme orientational disorder in the individual subunits of the protein has been readily characterized using (19)F NMR and the O(2) binding properties of the protein have been evaluated through the oxygen equilibrium analysis. The equilibrated orientations of hemes in alpha- and beta- subunits of the reconstituted protein were found to be almost completely opposite to each other, and hence were largely different from those of the native and the previously reported reconstituted proteins [T. Jue, G.N. La Mar, Heme orientational heterogeneity in deuterohemin-reconstituted horse and human hemoglobin characterized by proton nuclear magnetic resonance spectroscopy, Biochem. Biophys. Res. Commun. 119 (1984) 640-645]. Despite the large difference in the degree of the heme orientational disorder in the subunits of the proteins, the O(2) affinity and the cooperativity of the protein reconstituted with 2-MF were similar to those of the proteins reconstituted with a series of hemes chemically modified at the heme 3- and 8-positions [K. Kawabe, K. Imaizumi, Z. Yoshida, K. Imai, I. Tyuma, Studies on reconstituted myoglobins and hemoglobins II. Role of the heme side chains in the oxygenation of hemoglobin, J. Biochem. 92 (1982) 1713-1722], whose O(2) affinity and cooperativity were higher and lower, respectively, relative to those of native protein. These results indicated that the heme orientational disorder could exert little effect, if any, on the O(2) affinity properties of Hb A. This finding provides new insights into structure-function relationship of Hb A.
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Affiliation(s)
- Satoshi Nagao
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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Simonneaux G, Le Maux P. Carbene Complexes of Heme Proteins and Iron Porphyrin Models. TOP ORGANOMETAL CHEM 2006. [DOI: 10.1007/3418_006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Liu C, Chen QY. Fluoroalkylation of Porphyrins: A Facile Synthesis of Trifluoromethylated Porphyrins by a Palladium-Catalyzed Cross-Coupling Reaction. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500027] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Simonneaux G, Bondon A. Mechanism of Electron Transfer in Heme Proteins and Models: The NMR Approach. Chem Rev 2005; 105:2627-46. [PMID: 15941224 DOI: 10.1021/cr030731s] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gérard Simonneaux
- Laboratoire de Chimie Organométallique et Biologique, UMR CNRS 6509, Institut de Chimie, Université de Rennes 1, France.
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Nagao S, Hirai Y, Suzuki A, Yamamoto Y. 19F NMR Characterization of the Thermodynamics and Dynamics of the Acid−Alkaline Transition in a Reconstituted Sperm Whale Metmyoglobin. J Am Chem Soc 2005; 127:4146-7. [PMID: 15783177 DOI: 10.1021/ja043975i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A 19F NMR study on the acid-alkaline transition in sperm whale myoglobin reconstituted with a perfluoromethyl heme, 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2,12,18-trimethyl-7-trifluoromethylporphyrinatoiron(III), demonstrated that the thermodynamics of the transition is predominantly controlled by the stability of acidic form.
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Affiliation(s)
- Satoshi Nagao
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
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